


His Father's Son

by emluv



Series: Secrets, Lies, and Spies [5]
Category: Agents of S.H.I.E.L.D. (TV), Iron Man (Movies), Marvel (Movies), Marvel Cinematic Universe, The Avengers (Marvel Movies)
Genre: Agents of S.H.I.E.L.D. Spoilers, Captain America: The Winter Soldier Spoilers, F/M
Language: English
Status: Completed
Published: 2014-06-24
Updated: 2014-06-24
Packaged: 2018-02-06 02:56:20
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 4,577
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1841689
Author URL: https://archiveofourown.org/users/emluv/pseuds/emluv
Summary: <blockquote class="userstuff">
              <p>Tony sets his genius brain (and JARVIS) working on the many issues raised by the discovery of Hydra within the walls of SHIELD, and starts to form a plan to fix them…</p>
            </blockquote>





	His Father's Son

**Author's Note:**

> Fifth story in a series that will follow the various Avengers and agents of SHIELD through the fallout of the events of Captain America: The Winter Soldier, and now also the end of season one of Marvel's Agents of SHIELD. Contains spoilers for both the film and the series.

“Tony.”

 

Tony raises a hand and, with the flick of a finger, sends the holographic list he’s been reading into a rapid scroll. The frown perched on his face for the past twenty minutes deepens.

 

“Tony?”

 

“Hmm?” he says, eyes narrowing. He spreads his fingers in order to zoom into a section of the map that corresponds to a particular item on the list. “Oh, that’s not good,” he mutters under his breath.

 

Warm hands land on his shoulders before slender arms continue to reach around, circling him as slender palms stroke down over his chest. “Tony,” a throaty voice whispers in his ear, a silky fall of strawberry blond hair swinging into view just before lips press a kiss to his temple.

 

“Right,” he says softly, bringing his hands together in a emphatic clap that shuts down the holographic interface. Spinning on his stool as the arms loosen, he drops his hands onto gently curving hips. “Pepper, light of my life. What can I do for you?” he asks, focusing purposefully on his girlfriend’s amused expression.

 

“I heard from Jenkins. The dive team found Steve’s shield,” she says.

 

“That’s terrific. And it only took them, what? Four days?”

 

“Tony, you know they couldn’t start until we’d gotten permission from the city, not to mention half a dozen different environmental organizations and the Senate Oversight Committee, and then they _still_ had to comb through all that debris.” She looks moderately less amused, now.

 

“You’re absolutely right, sorry, my bad,” he says hastily, but he grabs her hips a little more firmly and tugs her close. “Forgive me?” he murmurs, giving her a quick kiss.

 

Pepper sighs, but her smile has returned. “They want to know if they should bring the shield back here or catch up with Steve in D.C.”

 

“Er, here. He and Sam are only down there for a couple of days, right? And so far, Sam’s place seems to be off the radar. Let’s keep it that way.”

 

“I’ll let Jenkins know.” She squints at him, no doubt taking in his extra layer of scruff and the fact that he’s in the same t-shirt from the previous day. “I’m not going to ask when you’ve slept,” she decides, “but have you at least eaten recently?”

 

He tilts his head side to side, knowing if he lies, JARVIS will likely rat him out. “I think I had breakfast,” he hedges.

 

“Today?” she asks pointedly.

 

He shrugs. “Depends, what day is it?”

 

Pepper just shakes her head. “I’ll have something sent up.” She glances toward the now-empty space where he’d been working on the data from SHIELD. “Any progress?”

 

“Maybe. I’ll let you know if anything comes of it.”

 

“All right. I’ve got a lunch meeting uptown and then calls all afternoon. You’ll eat, yes?”

 

“Yes, yes,” he nods. “I promise.” He pushes her gently back so he can stand and kiss her properly. “We’ll catch up tonight?”

 

She looks pleased. “Dinner in?”

 

“It’s a date.”

 

“What about Bruce?”

 

“He has a… thing. In his lab? Needs to stay close until midnight. I promised I’d order from the good Indian place for him, but we can have something else if you want.”

 

“Indian sounds perfect actually.” She turns to go, calling, “You behave,” over her shoulder.

 

He gives a little wave of acknowledgement, watches her retreat out of the lab and disappear into the elevator. Then he shifts backward, landing neatly on his stool, and spins around toward his work space. “Bring it all back up, JARVIS.”

 

~*~

 

It started as a search for loyal SHIELD agents caught out in the field, anyone who had been mid-mission when the shit hit the fan and had somehow avoided getting taken out, either by fellow agents revealed to be Hydra or by the targets of their operation. Tony’s first concern had been Barton, but he’d realized pretty quickly that Clint must have gotten a heads up – likely from Romanoff – because he’d switched on his StarkPhone and otherwise dropped off the radar. Which left Tony combing the intel for anyone else who might be in need of extraction.

 

He’d almost missed the spike in criminal activity, mostly because the incidents were wide spread and only occasionally reported as crimes due to their inexplicable nature – anything from reports of a woman whose presence caused everyone around her to fall asleep (useful in store robberies) to vague references to alien-sounding weaponry. But when a report popped up of an attack on a member of the Portland orchestra, involving odd power outages and energy surges, JARVIS had flagged it for Tony’s attention, and he’d started screening more carefully for similar events.

 

“Don’t tell me this wasn’t a SHIELD case,” Tony says, glancing between several accounts of the disturbance in Oregon, only one of which references the orchestra member, Audrey Nathan, by name. “Too weird to be anything else. And this has to be Coulson’s cellist. See if you can find some reference to her in any of the old SHIELD case files we downloaded.”

 

“According to the orchestra’s web page, Audrey Nathan does indeed play the cello,” JARVIS says. “She joined the company early in 2012, having previously been a member of a quartet based in Washington, D.C. Scanning the SHIELD data on our server now, sir.”

 

“Good JARVIS, do it.” He skims back over one of the more thorough reports, not that any of them include a whole lot of information. “Unknown assailant during practice at the theater, mysterious rescuers, victim woke to find attacker gone and power restored, yada yada yada,” Tony mutters. “Mysterious rescuers my ass.”

 

“Sir, in February, 2011, an individual named Marcus Daniels came to the attention of SHIELD. He possessed an ability to draw electricity from matter and conduct it through himself, acquiring unhealthy levels of power that he appeared unable to control. At the same time, he began to fixate on a musician named Audrey Nathan, following her, sending unwelcome messages and gifts, and refusing to accept her repeated requests that he leave her alone. Due to the unusual nature of his abilities, SHIELD flagged him as a danger to Ms. Nathan and to the public at large, and sent a team of agents, led by Agent Coulson, to intercede. Marcus Daniels was secured and taken to a SHIELD facility where the officially recommended course of action was to assist him in controlling his abilities and to find a safe, productive outlet for them.”

 

“Official? I’m guessing there’s the Hydra version of this story, too?”

 

“Indeed, sir. At a facility coded only as “the Fridge” in the files, Hydra scientists successfully worked at increasing Daniels’s power intake capacity while making no attempts at harnessing it.”

 

“Naturally. So I’m thinking that somewhere in the middle of this mess, someone let this guy go free. And he’s probably not the only one.”

 

“Unless the party responsible was seeking out Marcus Daniels specifically, it would seem likely that they simply released everyone who was being detained.”

 

“Can you access the names of everyone SHIELD had on lock down?”

 

“There does not appear to be a master list within the files leaked onto the internet, and the records you previously downloaded to the Stark Industries server are out of date. If I might offer an alternative, I can run a search on all resolved case files for the names of anyone remanded to the Fridge facility. It will, however, take some time.”

 

“Yeah, I know,” Tony sighs. “Do it.” He reaches for an apple off the tray someone had delivered at Pepper’s request, taking an enormous bite and chewing thoughtfully as he stares at the data blinking before him.

 

While JARVIS focuses his considerable power on making a list of apparent fugitives from SHIELD’s holding cells, Tony decides to go back to compiling a list of agents who might be in need of assistance. It’s a grueling process if only because he wants to access each agent’s status both at the time SHIELD’s records went public and more currently, and he doesn’t always like what he finds. He’s met a handful of agents over the past few years between the team sent with Coulson after he’d come back from Afghanistan and those he’d come into contact with on the helicarrier and in the aftermath of the battle against the Chitauri, and heard a few more names mentioned in passing, so those are the ones he plugs in first.

 

“Victoria Hand, deceased,” he reads aloud. “Felix Blake, long-term medical leave. Hmmm,” he murmurs, clicking on the incident file, which predates the whole Hydra reveal by only a couple of days. “Let’s see what happened… holy shit.” He scans the report, wincing at the appended medical records. He met Blake once, briefly, and came away with the impression of a bland stuffed shirt, but then he hadn’t thought much of Coulson the first time he met him, either; he’s learned his lesson about judging SHIELD agents by their tailors and reluctance to crack a smile. And anyway, he wouldn’t wish these sorts of injuries on anyone short of a Hydra sleeper agent, and from the looks of it, Blake is SHIELD through and through.

 

He backs out of the medical report to delve more deeply into the operation that led to Blake’s injuries. It’s obvious the entire file was originally locked at a high clearance level. Several of the agents involved are noted as having special dispensation to help in tracking someone labeled simply as the Clairvoyant – and doesn’t that send a chill down his spine – including a newly minted agent, Skye-no-last-name, who appears to have some serious hacking chops.

 

Eliminating the names he has already revealed are Hydra – John Garrett, who got taken out somewhere along the way, and Grant Ward, who seems to have been taken into custody in the last few days – Tony assembles a list of the agents whose status and whereabouts he has yet to uncover. There’s some reference to several of them working as a team, led by an agent whose name has actually been redacted aside from the letter C, but beyond that no indication as to which side of the divide they were on at the time of the op. Satisfied he’s got enough to start, he throws the list out into the waters of the internet to see what they’ve been up to since the Triskelion went down.

 

“Er, no, not possible,” he says, as search after search through the live SHIELD files leads to dead space. He flips back to the SHIELD files saved to his server, all of the data locked down within moments of it going public. And there they all are, employee files, education, training records, all of it. He frowns. “Hey, JARVIS? Switch over a minute, buddy.”

 

“Yes, sir, how may I be of assistance?”

 

“I need you to track the following names: Melinda May, Leopold Fitz, Jemma Simmons, Skye, just the one name – formerly known as Mary Sue Poots, wow, that must have sucked. All agents of SHIELD, all apparently part of some sort of mobile response unit. Their records are all accounted for up through the data dump, and then shortly after it they vanish.”

 

“Vanish, sir?”

 

“Vanish. As in, they no longer exist. Places they once were, they no longer are. I’m not talking killed, J, I’m talking ghosted. This Skye person’s a hacker, was with Rising Tide before SHIELD. I’m guessing she’s the place to start.”

 

“Sir, if this Skye has indeed managed to successfully delete the complete digital footprint of these agents and herself, there will be no trail for me to follow.”

 

“No one’s that thorough, JARVIS. It’s damned difficult to disappear. There’s something out there. We just need to find it.”

 

“Yes, sir.”

 

They each work quietly for the next hour, only a steady rock beat, volume set a few notches lower than usual, keeping the lab from being completely silent. Tony tries to make some headway with tracking other field agents still unaccounted for, but his attention keeps wandering back to the recently released SHIELD prisoners, and the potential dangers they represent.

 

He scrolls through the list of peculiar incident reports again. “Something’s bugging me about this,” he says finally.

 

“What troubles you, sir?” JARVIS asks.

 

Tony shakes his head. “This Portland attack seems to be the only incident to date where someone – and we’re assuming SHIELD – stepped in and solved the problem before the local authorities were called in. Everything else, either the police were there stumbling around or it never got past the conspiracy theory sites.” He tugs thoughtfully on his lower lip, eyes darting between the various files now spread out across the interface, attention shifting. “Why form a mobile response team?”

 

“Presumably to have a set of agents ready to move quickly when the situation requires, sir.”

 

“Yeah, yeah. But that’s pretty much all of SHIELD, right? They’ve got the helicarrier, there are bases all over the world plus some little satellite offices, and I guess these facilities like the Fridge that were top secret until everything went kaboom. When I got back from Afghanistan, Coulson was right there, already waiting at that press conference to get a debrief.” He shakes his head. “I’m missing something, here,” he mumbles under his breath.

 

With a flick of his wrist, he sends the files flipping, stopping them when he gets back to the reference to the mobile unit, at the start of the mission where Blake was injured. “The Bus,” he reads aloud. “Can’t be an actual bus, talk about slow mode of transport,” he muses. “Nickname for a plane, probably. So they travel around on this plane, trying to get a jump on situations. _Weird_ situations,” he adds, gaze lingering on the word Clairvoyant. “And they’ve got a hacker and a sniper – or did, before he turned out to be Hydra. Couple of scientists, lower clearance levels, so they must be brilliant to have made the cut.” He scrolls. “A pilot with some major previous combat experience. And an agent without a name in charge.” His jaw tightens as he stares at the letter C, blinking out at him from the file. “Fuckin’ Nick Fury,” he bites out.

 

“I beg your pardon, sir?”

 

“JARVIS, find me everything with Phil Coulson’s name on it,” he says. “Start with the files that refer to Agents May, Ward, Simmons, and Fitz, and include any mention of the Bus. Reverse chronological order, starting with the day the Triskelion fell.”

 

“Am I to assume this takes priority, sir?”

 

“Better believe it, JARVIS. Call me when you’re done. I’m heading down to the gym.”

 

~*~

 

Sweat runs down Tony’s face and neck, soaking the collar of his t-shirt and dripping from his hair where it curls wetly along his nape. He gives his head a shake, watches water scatter like rain drops, and pulls back to give the big bag one more hard right. There’s virtually no reaction, no movement, and that more than anything tells him it is probably time to take a break.

 

Tugging at the laces of his gloves with his teeth, he pulls off first one then the other, dropping them on the equipment table near the wall and scooping up a towel to wipe at his flushed face. He runs the soft terry fabric up and down, around the back of his neck, then scrubs it over the top of his head, sending his hair in all directions before finally dropping it in the hamper and taking a second, dry towel to drape over his shoulders. Then he grabs his water bottle and drains it in a few deep gulps.

 

“Sir?” comes JARVIS’s polite interruption.

 

“What you got for me?”

 

“I have not yet completed the current search, but Miss Potts has returned home and is placing your dinner order. She has requested that you let me know what you wish to have this evening.”

 

“Right, Indian,” he says, giving the empty water bottle a squeeze and pitching it into the trash. “Standard order. Extra naan, though, plain and a couple of the stuffed ones. Make sure you ask Bruce, too. Get him his own of anything that overlaps, since he’s eating in his lab tonight.”

 

“Of course, sir. And might I point out that you may wish to shower and change for dinner at this time, as delivery from Basera rarely takes long?”

 

“Yeah, quitting time anyway,” he agrees. “Let Pep know.”

 

“Very good, sir.”

 

When he reaches the apartment level, he can hear Pepper’s voice drifting from her home office. He heads into the bedroom and directly into their palatial bath, stripping off his wet workout clothes as he goes. Once in the shower, he stands under the multi-head streams of water, eyes closed, and tries to allow the tension to run off with the layers of sweat. He feels bombarded, between SHIELD and Fury and Rogers and now this whole Bus mystery, and part of him cannot understand where the hell everyone has gone. What’s the point in forming a team – under duress, granted, but he thought they’d pulled together pretty well in the end – if you can’t count on that team to come back together when the shit hits the fan. From where he’s standing, things look pretty shitty, and everyone keeps right on scattering to the four winds.

 

Rogers he understands. Cap’s obsession with Barnes has morphed into an obsession with Hydra – or, well, he supposes that was true during the war, as well, it’s just finally all caught up to the twenty-first century. And Hydra does need handling, he’ll give Rogers that. But Natasha’s vanished, Barton appears to have gone dark, there’s been no sign of Thor, and Bruce, while willing to discuss the situation with Tony until they’re both dizzy with exhaustion, has been pretty clear regarding his willingness to suit up for the cause.

 

But this mystery agent might be the key. Tony’s almost positive it’s actually Phil Coulson, that Fury somehow spirited him off and assigned him to some top secret project that required faking his death. But dead or alive, Fury’s off the reservation now and it’s time he stop calling the shots. If Phil Coulson’s death was enough to unite the Avengers once, maybe his resurrection can light a new fire under their tails.

 

He emerges eventually and dries off, then heads back into the bedroom to pull on clean jeans and a soft grey t-shirt, casual but plain. He wanders out barefoot to find Pepper curled up on the couch in her own casual wear – jeans with ripped out knees and a rose-colored tank in deference to the unusually warm day they’d had. She’s poking at her StarkPhone but stops when he draws near, tossing it on the coffee table with a smile.

 

“Hey,” she said. “Food should be here in five.”

 

“Great, I’m starving,” he says, dropping down next to her. “And yes,” he adds swiftly, holding up both hands to stall her questions, “I ate the stuff you had sent to the lab. But then I hit the gym, so… Starving,” he repeats with a grin.

 

Pepper leans in and kisses him, then pulls back and pushes a damp lock of hair off his forehead. “You look annoyed,” she decides. “What’s going on?”

 

He sighs and drops his head back on the couch cushions. “What’s not going on?” he mutters. “SHIELD and Hydra and Fury, oh my,” he intones. “Sounds like some sort of mythological action flick. ‘Revenge of the Titans.’” He lets his frustration color his expression for half a moment before shaking it off. “It’s hard to know what to tackle first,” he admits finally, sitting back up. “Honey, there are agents trapped out there in the middle of nowhere, and, near as I can tell, no one worried about getting them out.”

 

“Someone must be doing something,” she insists. “What about the Army?”

 

“Not according to Rhodey. They’ve got their attention all focused on the witch hunt. No one seems to remember that a good number of SHIELD’s employees are not and never were card carrying Hydra goons.”

 

The elevator door slides open behind them and Pepper pushes to her feet. “I’ll go get that. Why don’t you get us some plates and things.”

 

He nods and goes into the kitchen while she sorts through their order and sends the receptionist who brought up the delivery to take the remainder to Bruce. Rummaging through the cupboards, he locates a couple of plates and a stack of paper napkins, assorted utensils from a drawer. He carries it all to the small dining table they use when it’s just them. Staring at everything he’s brought out, he frowns, knowing something’s missing.

 

“What do you want to drink?” Pepper asks, unloading savory scented cartons from a large paper bag.

 

“That’s what I forgot,” he mumbles, turning to start back into the kitchen, but Pepper grabs his wrist, stopping him.

 

“Tony,” she says, and when he glances at her, she looks concerned. “Sit,” she urges him. “I’ll do it.”

 

He nods and takes a seat, reaching over to pry open the cartons and stick serving spoons into them, unwrapping the warm naan. When Pepper comes back with two glasses of iced tea, he smiles his thanks.

 

“Okay, why don’t we just talk about it, Tony?” Pepper asks, dropping down into her own chair. “I can see your brain’s going a mile a minute, and I know what it means. It’s not like the subject hasn’t come up before.”

 

“I know,” he says, avoiding her gaze in favor of spooning curry onto his plate. He doesn’t pretend not to know what she’s referencing. “Last fall. And you didn’t want me to do it, so I didn’t, because you thought it was a bad idea.”

 

Pepper sighs. “Because you were still recovering from heart surgery!” she points out. “And it didn’t seem like Thor needed your help. Whatever was going on, he solved it on his own. There was no need for you to go jetting off to London while you were still healing.”

 

He risks peeking up at her, passing her the carton so she can serve herself.

 

Pepper takes it with a little sideways tilt of her head. “And now it’s six months later, and you’ve had a couple of clean check-ups and this all seems much… broader in scope,” she finishes with a nod as she sets the carton down. “I can see how crazy this is all making you,” she adds with a little smile. “And Tony, you were the one who blew up all the suits. I never asked you to do that. I appreciated it, but… I didn’t expect you to stop being Iron Man entirely. I just wanted you to be a little less…”

 

“Insane? Manic? Co-dependent on my creations?”

 

“Yeah, well, maybe a little of all those,” she agrees. “You weren’t dealing with the things that were really bothering you after New York, you were filling time. Building playmates,” she continues softly. “That’s changed.”

 

He exhales harshly. “This situation, Pepper, I just feel like I need to do something. Contractor, consultant, whatever the hell I was to SHIELD, that’s my father’s legacy that’s falling to pieces, and so many lives are on the line. I can’t just sit here and watch,” he says.

 

“I don’t think you should, either,” she tells him. “So how far along is it?”

 

“Is what?”

 

Pepper smiles. “The Mark whatever-the-hell-number you’re up to. I know you started rebuilding it during the thing with Thor in Greenwich, and that you stopped after we talked. But you didn’t get rid of it, did you?”

 

“No, I didn’t,” he agrees. “You mad?”

 

“Of course not. It was never a line in the sand, Tony. I just didn’t want you endangering your health.”

 

His lips twitch. “You’re the best, you know that, right?”

 

“I might have heard it once or twice,” she says. “So?”

 

He gives a shrug. “Needs another half day’s work, maybe.”

 

“Then I guess you know what tomorrow’s project is, don’t you?”

 

“I guess I do,” he says with a smile.

 

“But tonight? You’re mine, Tony.”

 

“I’m always yours, Pepper,” he replies.

 

~*~

 

It’s still dark when he wakes. He lifts his head from where it’s smushed into the pillow and stares at the clock. Nearly an hour until Pepper’s alarm will go off, but he’s gotten a solid five hours of sleep – well within acceptable parameters, at least for him – so he crawls carefully out of bed and goes to pull on some clothes.

 

In the kitchen he fills a mug with coffee and leans against the counter as he drinks, letting the high-octane caffeine do the job of waking him the rest of the way. Half a cup down, he calls out softly to JARVIS. “So what do we have?”

 

“The agent referred to by the letter C appears to be in charge of all missions pertaining to the Bus and its team. His full name is redacted on all after action reports, supply requisitions, and other pertinent forms. His signature on scanned hard copies, however, precisely matches that of Agent Coulson in both the word agent and the slant and shape of the initial C in his last name.”

 

“Goddamn Nick Fury and his games,” Tony breathes. “What else?”

 

“The files for the agents you requested – May, Simmons, Fitz, and Skye – were only deleted from SHIELD documentation and any outside records that pertained to their years with SHIELD. In the cases of Agents Fitz and Simmons, both were apparently recruited quite early to SHIELD Academy, and so there remaining records date back to the years before they entered the equivalent of high school. Birth records, early education and so on, still remain for all the agents, with the exception of Agent Skye who, according to the SHIELD data we maintain on the server, came into SHIELD custody as an orphaned infant rescued during a classified operation. The digital files are incomplete; I can only assume there were hard copy records that were classified at the highest level.”

 

Tony frowns. “Okay, we’ll definitely be revisiting that later. Right now I’m more interested in Coulson. What about his records?”

 

“Agent Coulson’s records were deleted in the same manner as the other agents’ documentation, sir, which begs the question, why delete both the employment and personal history of a deceased agent.”

 

“Because he’s not dead,” Tony replies, though the AI had clearly not been asking. “Okay, JARVIS, I need to know everything possible about what happened to Agent Coulson after New York. And then I want to know where the hell he and his little team are.”

 

“Very good, sir. Are you planning to share the news of Agent Coulson’s survival with the others?”

 

“Not yet, and not Pepper either, J, so no snitching. I’d prefer to keep it between us until I can find some proof. Preferably Coulson himself.” He takes a long drag on his coffee. “Is Maria Hill around?”

 

“I believe she returned from Los Angeles, sir, but is scheduled for further debriefing in Washington today. She should be back in the New York office tomorrow.”

 

“Set up a meeting, just the two of us,” Tony says. “I think it’s time Hill and I have another little chat.” He drains his cup and reaches for the pot. “Screen everything incoming for the next few hours. Time to go finish the new suit.”


End file.
